Is the bottle formula? If so, it might not be sitting right with him. Otherwise, my guess is that you either need to wait him out or fully let him cry it out.
First of all, it doesn't sound like there's any reason to be careful not to let him nurse to sleep. The point with that (from no cry sleep solution as well as from all of the cio books) is that if they fall asleep on their own at bedtime then they are more likely to get themselves back to sleep when they wake at night. I'm sure it works for some, but it certainly didn't work for my kid and isn't making a difference for yours. Oh, and we also had rock solid bedtime routines--another magic sleep fixer that didn't do much for my kids.
Here's my experience with my 2 boys: older son co-slept and I night weaned him at 2 years. He very rarely went longer than 1 3-hour stretch. At 5 he'd still be co-sleeping every night if given the option, he's just that kind of person who sleeps better when he's close to someone. Some would say it's *because of* the early co-sleeping, but then there's my younger son.
He's almost 2.5y now. I mostly co-slept early on with him, then it was start off in the co-sleeper next to our bed until he woke. He slept longer and longer stretches, then got sick at 3-4 months and was waking every couple hours every night. Then, by 6 months, he wouldn't sleep next to me anymore--I kept trying but he was so restless until i'd put him in the crib. So with having to actually get up when he'd wake, I was hating night time by the time he was 8 months old. I read the books, but it seemed like falling asleep on their own was the big thing to do (and assumption that it must not be happening if they weren't sleeping thru the night) but my son had been doing that since 2 months. Just because he wouldn't fall asleep nursing, not because I wouldn't do it.
So at our 9 month appt my ped gave me a rather shocking suggestion (she knew my sleep woes with older son but never gave suggestions or comments b/c I never asked for, or wanted, it): She said put him in his own room, get him to sleep any old way, go in the first time he wakes up and tell him "i love you and will see you in the morning," and don't go back until 6am. She said he might cry off and on for 5 or 6 hours (not the "up to 30 minutes" that the cio experts like to spout and make it seem like it's easy if you do it right).
I couldn't bring myself to do, and couldn't and couldn't, and then decided to try it. When he was 13 month. There was no improvement and I was not enjoying my life, my kids at all b/c I was so sleep deprived. I was ready for a big ordeal, told myself I could change my mind at any time, we'd just see how it went. And I bought a video monitor so I wasn't paranoid that something was really wrong when he cried. I was prepared for him to be really clingy the next day, too.
So he wakes up after his usual 3 hours, cries (more like complains, it was definately not his freak out cry) for all of 10 minutes. Wakes a while later and cries for 5 minutes. Wakes up at 6:30, happier than ever and completely unaffected. Then next night was 5 min and 2 min, the next was 2 min, then done. I was shocked. But it just turned out that not only did he not want to sleep next to me, he didn't want to be in the same room. :-) He wanted his space.
In no time he was nursing and then i'd want to walk him around and sing/cuddle, but he'd just reach for the crib.
We've had to do it again a few times, like after illness or teething (he gets into habits very quickly, in all aspects of like). And he's always happier and better rested once he's sleeping thru the night. I never ever in a million years thought i'd let a child of mine cry it out, never really thought i'd use a crib even. Then I had a child that needed something other than what i'd planned.
Good luck with whatever you decide, I know it can be hard to think clearly when you're not getting the sleep you need!