I had 88 in the small blind and raised 3x big blind to 150. I appeared more like an aggressive player who raised preflop frequently when playing heads up with this guy. We'd been playing for about 4-5 hands until this one.
X called (lets call my opponent X)
Flop came 549 rainbow
X raised 250. I called
Turn came 6
X raised 300. I reraised 300 to 600. X called
River came 9 (no flushes possible)
X moved all in about 950. The pot is now 2950.
Should I have called or not? ( I had about 1100 left)
(no reads)

It's a tough spot, but I think making the call would be the wrong choice. He played the hand like he was very strong, so I would have put him on a over pair, maybe even the 9 since he just called your reraise on the turn, and shoved the river.