I never see the need to bomb Japan. I would usually rather have two more submarines to secure SZ 6, to blow up the IJN, or to convoy than I would another strat bomber in the pacific.
You can hurt Japan’s economy by being aggressive in other ways, and you usually have a very real threat of a Japanese counterattack devastating the allies while you do it that is always looming over you. A strat bomber can’t defend your fleet. Another fighter, 1.5 destroyers, or a couple subs can, and they can also take part in a naval attack just like the bomber could.
If you’re already at the point of having turned the tide in the pacific, it’s not worth your time trying to bomb an already-crippled Japan or to try and invade a turtled-up Japan. Just wrap them up enough so that ANZAC/China can keep them busy, then hurry your ass up in the Atlantic.
That’s not to say strat bombers aren’t useful in the pacific. They surely are, and one or two can clear destroyer blocks, or threaten sea zones that you couldn’t normally threaten (as to keep undefended transports from moving around), or help with some island hopping by not putting your navy in harm’s way to support a lone transport + infantry drop. They can also be built in western US for a one-last-build before a big fight since they can fly quite far to make it to the next round’s combat. But to plan on bombing Tokyo? Meh.
And to think from where is best? That all depends where your bombers night need to go next round. Mainland asia might be able to get them to Moscow to be defense fodder there (Jehol, maybe others?). The far eastern USSR territories might be your only option for a turn, and therefore would be best by definition. Iwo Jima is nice in that it’s easy to defend and is close, and reaches much of the Pacific. But it all just depends on that particular game since this kind of concern is, at best, an A3, but very probably an A4-A6 situation, and too much can change by then to give an answer.
Finally, if you do begin to win the Pacific, your bombers, if any are still in the pacific, are some of the first units that leave the theater for the Atlantic side, because they can get there and be effective faster than anything else that you have.
If I’m wrong on this one, and have been overlooking something that is vital to the pacific war effort by not bombing Tokyo, please enlighten me.