A.C.
When we had a similar issue, my sister gave me some advice from a book (by a pediatrician sleep expert) that suggested - counterintuitively - to put the kid to bed earlier at night. This actually worked for us for awhile. The technique has something to do with promoting longer deep-sleep cycles. I had been putting my daughter to bed later and later (e.g. 9-9:30 instead of 8:30)trying to get her to sleep longer in the morning and it didn't work. We finally started putting her to bed earlier (7:30) and she actually slept longer. You can try it . . . However, this was back when she was more like one and a half to two.
Now that she is two and nine months, she does not seem to need as much night-time sleep and we are putting her to bed later again. A new problem is developing: 2-hour naps at school that I don't think she needs anymore (I also work full time and don't have control over the length of her day-time nap). So that is another possiblity - maybe your son is getting too much nap during the day?
Another possiblity - is he disturbed by your getting up to check on/nurse the 3-month-old and is there a way to alter the sleeping arrangements so that doesn't happen?
See if your Dr. has any suggestions too. Good luck!