i have a hard time saying it, but craigslist is definitely your best starting point (keeping in mind all of the disclaimers people give about the postings on there...if you dont know them, i'll gladly fill you in)
other than that, i think your best options are:
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www.rent-direct.com: they charge a fee, but i believe you get access to a lot of 'no fee' postings you'd never find in other places
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www.eberhartbros.com: mostly UES, but solid places...if you check the site right now they have a 1-br not too far from fordham on UWS for $1850/mo...listings change periodically and they are all no fee/very legit
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www.aimconyc.com: slightly more expensive, but no fee/legit
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http://howtorentinnyc.com/review.php: some unreliable links/etc, but may have some luck here going directly to mgmt companies
-check realtor's websites...the firms i've had the best luck with in the past are Corcoran (a bit higher end), Halstead (also a bit higher end), Bond, Century21, and Prudential Douglas Eliman...all have ample listings/pictures on their websites, so i definitely suggest you peruse these
as far as a website for commute times,
http://www.hopstop.com isnt bad...it will atleast give you a general sense of subway routes/connections/etc
EDIT:
http://www.triptropnyc.com
people have also been passing this one around for commute times