Kingpin could easily be the leader.You need someone with alot of juice to be able to get all these villains together.You could even count Kingpin as a member so you wouldn't have to worry about the budget on special effects.
Maybe Peter has witnessed the Kingpin kill someone and the the Kingpin can't find Peter to kill him because Peter has been scooped away in the witness protection so he can testify and put Kingpin away for murder.
So the Kingpin holds the city hostage with his muscle.He could have Hydro-Man guarding the outer part of the city not letting anyone in or out of the city,he could have Electro cause a blackout where even generators and flashlights won't even work,he could set a curfew and anyone who is out will be killed by the Vulture and the Hobgoblin who are patrolling the skies,and Scorpion could be out hunting for spidey.
But spidey isn't in the city since Peter was wisked away to be put into the witness protection.Kingpin could show pictures of Peter saying that if anyone kills Peter that the city will be released from his captivity.
Then Peter convinces the witness protection to give him to the Kingpin and they basically have no choice they think,so they let him go.And when Peter gets to the city two of Kingpin's villains(Vulture/Hobgoblin)could take Peter to the hideout of the Kingpin,because Kingpin wants to kill him personally.
When Peter is in the hideout and Kingpin pulls out a gun and is about to kill him,Peter does some spidey acrobatics and Kingpin and the two villains are surprised that this kid is spidey.
Kingpin is calling his other three villains(Hydro-Man,Electro,Scorpion) back to the hideout for backup as Kingpin is shooting at spidey with a gun as Vulture and Hobgoblin are flying all around in the room as they are fighting spidey.
The Scorpion comes breaking through the door and shoots acid from his tail at spidey while spidey is fighting Vulture and Hobgoblin.Spidey dodges the acid when his spidey sense goes off and the acid hits the Vultures wings where they melt completly off,then the Scorpion swings his tail at spidey and spidey dodges the swinging tail as well,but the Vutlure gets hit with it and is sent crashing out the window and falls down fifty stories to his death.
Then one of Kingpin's bullets hits one of spidey's shoulders and one hits Hobloblin's glider and makes the Hobgoblin's glider go bursting full speed out the window,spidey jumps to the ground as it goes flying over him,and spidey shoots a web at the Kingpin and the other end to the Hobgoblin's glider where the Kingpin is dragged out of his office screaming as the Hobgoblin is dragging him away.
Spidey jumps out the window to go after the Kingpin,and the Scorpion follows.Spidey and the Scorpion have a huge fight on the rooftops as spidey is trying to not lose sight of the Kingpin.
Then the Scorpion hits spidey with his tail and spidey is sent falling off the rooftops and Scorpion goes after him and they fight as they fall(like spidey and Venom did in SM3) and they land on the hood of a parked car that is parked on the side of the street.
There both laying there on the crumpled car,and the Scorpion is hurt bad where we see a piece of metal is sticking out of his stomach.Spidey rolls off the hood of the car and walks to the trunk of another parked car and is leaning over trying to catch his breath until his spidey sense goes off again.
Spidey jumps onto the side of the building as a bolt of electricity hits the parked car he was leaning on and the parked car goes flying into the air and comes back down and lands on the Scorpion.
Electro stands in the middle of the street and starts shooting at spidey who is on the side of the building with bolts of electricity.Spidey ducks behind another car as the car is being shot full of holes looking like swiss cheese.
Spidey web zips under the car and across the street under the Electro's legs and underneath another parked car on the other side of the street.Then spidey shoots a web onto the Electro's back and yanks hard on it.
Electro crashes through the window of a parked car.As spidey is getting to his feet the car door is blasted off its hinges and the door flies over and hits spidey.
Spidey and Electro are fighting,spidey is jumping on the side of the building,jumping onto cars,jumps onto a fire hydrant.
Then as spidey dodges another bolt of electricity,the bolt of electricity cuts the top of the fire hydrant off sending water shooting into the air,and the water comes back down splashing all over Electro frying him.
As spidey is on the side of the building watching this a fist formed out of the water punches spidey and spidey goes through the wall.Spidey is fighting Hydro-Man inside a building that happens to be an ice rink.
They have a huge fight,during the fight.Hydro-Man busts open the ice on the rink and uses the water in it to turn into a giant Hydro-Man.They continue to have a huge fight where spidey is basically doing some cool spidey acrobatics trying to dodge the giant fists of water.
Until spidey sees the control box on a wall that makes the water turn to ice for the skaters.Spidey shoots a web ball at it and Hydo-Man becomes frozen where people skate on him forever.
As spidey is walking out of the building he is shot in the stomach and falls to the ground.As spidey looks up he sees the shadow of the figure illuminated as the Kingpin steps into the streetlight.
The Kingpin says some words and pulls the hammer to the gun to finish spidey.Spidey shoots a web ball into the muzzle of the gun,and the gun explodes in Kingpin's face when he fires it killing the crime lord of the city.
And you find out later that Hobgoblin was arrested when he was knocked out when he crashed into something.