An effective anti-ninja strategy is to strengthen inner defenses by not leveling outer defenses until needed. Actually, this allows towers to attack more overall since they damage less, meaning they continue to rack up experience quickly, until you're ready to level them. Makes a huge difference.
Wow. 4.6?? Holy crap. This game is alright, but the TD genre is flooded and, while this game is well executed, it brings nothing new to the table whatsoever. 2/5.