Best way to beat ninjas: Put a temple as early as possible to force them into an early stealth. Put crypts on high ground, or near gems, and they'll burst damage the ninjas down when they pop from stealth. Also, save your frenzies and meteors for ninjas.
Great game. Crypts appear to be the most powerful overall though, since they level fastest (biggest range + burst of damage = lots of fast levels at other towers' expense). Not positive of a balanced fix, but decreasing their xp gains about 20% and increasing both other towers by 10% each might help
Random tips:
Build a web in 1 corner, so that when the opposite corner is destroyed, your web survives. The more attachments to the 2 branches touching your corner, the better, build lots of random attachments when your webbing is full. Eventually build out along the edges.
Samboy, towers fall over because they aren't structurally sound and are at an unstable equilibrium, means the physics engine is more realistic in this game.
Cool concept but not enough user control. Also you should only lose if white balls = 0. Sometimes I lost when opposite colors hit each other, even if I had extra white balls.