Aleisha, your pediatrician is giving out *horrible* and UNPROVEN advice... why on earth would he recommend formula if you've been successfully breastfeeding all this time?!?! I just don't get that at all. If you really want to give him a bottle before bed instead of nursing him down (completely complicating things, but even so), simply pump your breastmilk and feed it to him via bottle. Of course, nursing is a heck of a lot more natural, easier, cuddly, and healthy. As far as the formula recommendation, not only would you potentially be introducing cow's milk or soy into his diet (formulas are based off of one of those things) which could result in his having an allergic reaction and sleeping WORSE than before, but study after study has shown that "filling up a tummy" with food is NOT proven to help them sleep any better. Period. Why wouldn't your ped recommend a a bottle of expressed breastmilk and/or a small bedtime snack before going straight to formula? If I were you, I would really, really just tune out any future breastfeeding "advice" (if you can call it that) that your ped gives you - clearly, he's WAY behind the times with respect to supporting the mother/baby breastfeeding relationship.
Also, your doctor's recommendation to let him "cry it out" is just his personal opinion - NOT medical fact. I hate it when pediatricians try to pass off their personal (NON-medical) parenting opinion as medical fact. UGH. How do YOU feel about your son's nightwaking? Does it bother you to nurse him back down 3x a night? If it doesn't bother you and you and your son are find with it, then there is NO need to change it. You're being a wonderful mother to respond to his needs both at night and during the day - other babies should be as lucky as yours! :) Now, if you're feeling exhausted by the nightwaking and YOU need that to change, there are definitely gradual steps you can take to change the nighttime situation: highly recommend Elizabeth Pantley's "No Cry Sleep Solution" that you can check out of your local library for free. If you want a more aggressive approach (but not anywhere near as crazy as "sure, let him cry til he pukes!") check out Kim West's "The Sleep Lady" book.
In the end, YOU know your baby *far* better than your pediatrician - and breastfeeding and being a responsive parent at night as well as during the day? Well, these ARE very, very healthy ways to care for your son. Don't let some misinformed, behind-on-the-current-research pediatrician convince you otherwise!