From my experience: spots everywhere, all impossible to skate because every building has a crew of security guards that will come kick you out, most of the time before you can even get on your board anywhere near the plaza they're assigned to. You get longer windows of time at night (and those are usually very short too). They won't give a shit if you skate outside the area they are supposed to guard, though; also the consensus in basic law enforcement in Japan seems to be that if you do something wrong, then it's obviously because you don't know it's wrong so it's their duty to come and warn you regardless of how much you realistically should have known - they give you the benefit of the doubt, do not try to argue and always just comply because the way administration and whatnot is handled over there seems like a living nightmare to get caught in; also a lot of the security guards have radios and will warn more cops in the neighborhood if you try to skate off or talk back, basically you'll just bring more bullshit upon you. The actual cops might try to block you if they see you ride down a street or something because street skating just isn't something one is supposed to do there and is considered hazardous for the most part, some care more than others.
General public will most often not have a clue of what the fuck it is you're doing outside of a skatepark, and see you as potentially dangerous but trust your control. If your board shoots out or someone suddenly gets in your way, they just won't know how to react as well as in occidental countries, so they will fully take the hit and you will be the asshole of the story.
If in Tokyo, check out Fat Bros to meet people and get directions, and Morita's FESN Laboratory, both skateshops in Nakano.