V.S.
Hi S..
My daughter will be 3 in January and also was a great sleeper very early and now wakes up everynight like your son. I discussed this with the doctor he asked me if her eating habits have also changed and they have she went 3 days without wanting to eat just drinking water and maybe a few cheerios even lost 2 lbs (she had them to spare , she was weighing 42lbs). Well he told us that all those changes in her were due to growing pains, apparently they hurt more at night and what not (he didn't explain the change in eating though he didn't seem worried about it.) We just give her some water when she wakes at night and tuck her (and her baby) in again and she goes right to bed sometimes she'll get up again but we just go through the motions all over about 3days of doing this and then she'll sleep well or minimize the wakings for 2 days and then we go back but the doc said it should be over soon... Maybe talk to your pediatrician about it to see if they agree.
Oh and she also rarely naps...
Hope this helps and you find the root to this soon...