First of all congrats! on both having yoru baby and sticking it out with the breastfeeding! Both huge tasks in themselves!
Babies have to learn EVERYTHING--including how to fall asleep and self-soothe...if he learns to fall asleep nursing, then that is what he'll learn and expect, but if you TEACH him to fall asleep on his own, both you, your baby and your family will be happier in the long run. And lucky for you, 3 months is a perfect time to start. It's hard with BFing, but with a nice routine, and a few weeks of hard work, not only will you be able to teach him to fall asleep without the nipple, but also to sleep through the night without needed to nurse! I'm talking 8-12 hours. plus 3 naps---really.
Luckily, there are methods for you to choose from other than the Ferber or CIO methods.
Two more middle of the road approaches are:
Secrets of the Baby Whisperer: How to Calm, Connect, and Communicate with Your Baby by Tracey Hogg http://www.amazon.com/Secrets-Baby-Whisperer-Connect-Comm...
and
Good Night, Sleep Tight: The Sleep Lady's Gentle Guide to Helping Your Child Go to Sleep , Stay Asleep, And Wake Up Happy by Kim West and Joanne Kenen http://www.amazon.com/Good-Night-Sleep-Tight-Helping/dp/1...
I've known quite a few moms that have taken either approach in these-both that BFed and Bottle-fed and ALL of them (including myself) have had wonderful results...but it is a matter of reading the books and following their plans (both much more gentle than CIO). Both are available from the library BTW.
I personally used the Baby Whisperer, but Good Night Sleep Tight wasn't out when I had my son--since then I've known many moms that praise that book even more than the Baby Whisperer. Anyways, my now 2 1/2 year old has slept 10-12 hours a night since he was 16 weeks old (excluding nights of course when he was sick or teething or something) and by 6 months was a great napper--which is still is at 2 1/2--I get very little resistance from him at bed or nap time...(it's all about teaching them how to self-sooth and what to expect)
Anwyay, good luck!--read up and see if either of those books offer solutions and plans you can do!