Hmm....Hulk was getting the upper-hand on the helicarrier fight, tossing him around like a basketball, but I wouldn't say he was kicking Thor's ass. Thor wasn't giving it his all.
In fact *NEITHER* character was going all-out.
Yes, Hulk was enraged but the punch that caused Thor the slight nose bleed was nowhere near the force of the punch that took down the leviathan. That would've seriously hurt Thor, much the same way that massive lightning strike that destroyed multiple leviathans and many Chitauri would've seriously hurt Hulk too.
From what we've seen so far, they are pretty much equals in the MCU. Hulk's superior strength and durability is balanced out by Thor's wider variety of powers, hammer, and flight. Until/unless Thor gets the Odin Force, of course.
Just my opinion