Easy flop raise.

This is the kind of predicament you can find yourself in by waiting until the turn with only a pair of nines in a three-way pot.

There's merit to waiting for the turn with intentions of raising any good card or folding any bad card. If you call on a bad card, however, it really defeats the purpose of not raising the flop.

That being said, you also need to call the river raise. He has an overpair often enough for a call to be worthwhile. Also, keep in mind that you didn't play this hand like you have a nine, so he might be raising the river more lightly than you think.