The war in the Pacific would have eventually been won, it just probably would have taken a little longer and Japan would have remained more or less untouched a little longer as well.
Without the B-29 (barring another large aircraft didnt come along) I would say decent full scale bombardment wouldnt occur until a lot of mainland China and Korea had been captured allowing use of shorter ranged aircraft like B-17's, B-24's and Lancasters.
I remember reading somewhere (I believe on the childrenofthemanhattanproject site) that scientists didnt really know exactly how big the bomb would be at first, but even then plans were being developed to get the bomb to a target. One method considered was delivery by a boat. From what I remember it involved getting a craft in a harbor. Pretty tough to even do that without even considering Japanese defenses as well as control of the thing. Still I am sure it would have made it.
Another option once it was found that the bomb was able to be carried by aircraft was the Lancaster. This was even considered, here is an excerpt from an article:
"Ramsey quickly concluded that there were only two Allied bombers capable of carrying both weapons: the Boeing B-29 (if suitably modified) and the Avro Lancaster. The Lancaster had ample room internally, and it was a prodigious weight lifter; it almost won the contest. In fact, Ramsey traveled to Canada in October 1943 to meet with Roy Chadwick, the Lancaster's chief designer. As luck would have it, Chadwick had crossed the Atlantic to view Lancasters being built at the Avro Canada works in Toronto, and Ramsey seized the chance to show Chadwick some preliminary sketches of both the gun and the implosion weapon casings. Chadwick assured Ramsey that the Lancaster could accommodate either bomb and promised whatever support might be needed, but he was well-used to wartime secrecy; Chadwick did not ask why the weapons had such unusual shapes.
When Ramsey returned to the US, he recommended to Parsons that the Avro Lancaster should be seriously considered. Apparently General Groves had not yet asked for US Army Air Forces support, however, and a different kind of detonation took place when the Chief of the USAAF, General H. H. 'Hap' Arnold, received word of the proposal. Arnold had been personally briefed on the programs importance by the Army Chief of Staff, but Arnold made it clear to Groves that, if any atomic bombs were to be dropped in combat, a USAAF-crewed B-29 would deliver them. With that proviso firmly established, Arnold willingly endorsed the Manhattan Project's request for USAAF assistance."
from: cybermodeler.com/history/silverpl/silverpl.shtml
The book "One Hundred Years of World Military Aircraft" covers this as well.