Pretty much what you've indicated:
time bonus (for "advancing" the next wave)
Value of coins & towers
These are then totted up and multiplied by the level difficulty.
I believe there's four difficulty levels. You can keep "resetting" after that point, but I note that the multiplier doesn't seem to increase after four.
A couple more things:
1. The "introduce this power-up" levels (where you get to test the various power ups) also add to the score, including application of the multiplier;
2. I'm not sure, but I think the number of gems might impact the total score (eg. 8/10 gems = 80% of score) etc. Could be wrong though, I've not bothered with the maths, just noticed my score seems a lot lower when an evil jelly sneaks through.