I have never woke either of my children on purpose.
My three month old has slept in 5 hour stretches at night since day 1 and she is growing like a weed. Thankfully she is a very effective little nursling. I put her to sleep downstairs at about 8, right after my two year old goes to bed. Then when I go to bed around 10 or 11 I bring her upstairs with me and change her diapers, swaddle, and feed her for a few minutes. Then I lay her down in the co-sleeper and she will sleep until 6-7. I feed her then and she is usually back down until 9-10.
Have I mentioned she is the most perfect baby that was ever born?
If you are going to wake him at all I would wake and feed right before you go to bed yourself for the night. I would not get up every three hours throughout the night. If he is sleeping, he wants to be sleeping. As long as there are no medical issues, I would let him sleep until he wakes to eat.