(Much of the following information is gleaned from various sources, mostly Wikipedia, and also the content of John and Yoko's music and art that I've seen and heard. I haven't read any biographies of John, Yoko, or any Beatles-related figures for that matter, so I don't know if there's information I haven't heard, but this is the impression I get.)
I somehow doubt he would have gone back to Cynthia, because as far as I'm aware she no longer had any interest in him whatsoever. May Pang would probably be more likely, as he did say at one point that he was the happiest he'd ever been when he was with her; also, according to Pang, Yoko was indeed manipulative of John prior to his relationship with Pang, and she helped John learn to deal with the emotional scars that allowed Yoko to treat him thusly. However, there's no telling how much of this happiness was due to the huge amount of alcohol, pot, and heroin he was using at the time, or how much of Yoko's cold treatment of him was due to her own drug addictions and inability to cope with her own scars (John wasn't the only unhappy one; Yoko did, after all, have her own share of tragedy in her life, having lived through the fire-bombing of Tokyo and subsequent homelessness, as well as having to deal with the kidnapping of her daughter, Kyoko, by her ex-husband). We do know, however, that Yoko eventually reached out to John and suggested that they clean up together, and presumably Yoko was doing some deep thinking about herself and her past as well during that time. As happy as John claims to have been, he took that offer and got back with Yoko. Someone in my "Why does everyone hate Yoko?" thread said that she drugged him with cocaine so he could manipulate him throughout their marriage, and that Yoko was somehow at fault for not helping John quit when she knew she had the power, but this is all false. If John ever used coke, it was only briefly, for one thing. Heroin was his drug of choice, and Yoko used it as well, until they both helped each other to quit the habit, as well as other drug habits, in the early to mid seventies. By the time they raised Sean together, they were both clean.
Also, contrary to John's comment about his happiness with May Pang, in 1980, which I can only assume was a later date, John said that in 1980, around the time of Double Fantasy, he was the most content he had ever been in his entire life.
These could both be true, of course. I know a former alcoholic/drug addict, who spent 30 years basically on the streets or in friends' homes. He said he was extremely happy at that time; someone who's constantly using drugs is always happy, until of course they have a dry spell where they can't afford any drugs or booze for a little while. He also says, however, that now that he's been clean for a few years and his life seems to be getting a little better, he's very content. John may very well have been the same way. He was ALWAYS high when he was with May Pang, so his addled brain may have been incapable of producing negative feelings during that time. So no, he wasn't as happy with Yoko as he was with May, but I don't think he would have traded his life with Yoko and Sean for the world. The songs on Double Fantasy seem to indicate this.
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So what do I think John would be doing if he were still alive today? I think he and Yoko would have continued to make wonderful art and music, continued to work toward world peace, and I think John would be just as much in love with the Internet as Yoko is today. I think they would be sending public love notes through Twitter.
I also think Yoko would have likely eventually eased up on Julian and John's other family a bit, at least due to public (i.e. tabloids') pressure on John's behalf, if not due directly to John's desire for her to do so. Unfortunately, without John here, the tabloids have nothing to latch onto. Nobody really cares about what Yoko thinks or does these days except for her own fanbase, it seems.
