As a side note, would your answer change at all if you happened to have J-10?
Interesting question...well, you're no longer worried about TT, and you're less worried that he has AJ or JJ.
It would come down to whether he would give up on 99 or TT if you called a flop bet - I'm inclined to believe he would not...that a reasonable player who led out a continuation bet on the flop, and got called, could still believe his 99,TT, maybe even 88 are good....and fire again at the turn. Now, hero with top pair mediocre kicker doesn't know where he stands.
I think I'd raise with TJ to define things some more (or take the pot right there). I think raising an additional 2000 will likely be cheaper than a call you'd need to make on the turn for similar information. If you just called the 1000 on the flop, the pot is now 3500, so a turn bet of 2500-3000 could be expected.
On the other side of the coin, if you are behind you have more outs than 99, so I wouldn't call a call terrible - I just think it leaves you more in the dark.
With 99, if you get bet on the turn the only hand you're beating that he "might" bet with is 88..otherwise, you're fairly certain you're dead. With TJ, there's a couple more possibilities of hands that you beat, and it also reduces the possibilities of a couple hands that beat you.
(I'm making an assumption that 66-22 are out of the picture - and that may be a bad assumption)