quadruple cocktail for apartment searches.

hyperdia (pronounced hyper-DIE-uh, it seems)
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Japanese Wikipedia
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Google Maps (Japan)
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Able (or whatever search site you choose)
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an alright start.

If Japanese Wikipedia seems like the odd man out, look at this. Each train line (JR, metro or otherwise) has a wiki page, from which you can click each individual station's page. With that you've got all the links and some other useful info (like the continuity of train lines).
Knowing all the stations relations to one another lets you know where to search at Able, and Hyperdia will let you know the last trains, and any unforseen craziness to the commute (like interrupted lines, or express trains).
Google maps is just sort of icing on the cake, to give you an idea of the neighborhood.

I'm looking at kosuge and other places on the isesaki line, kawaguchi, and toda right now.