I get up to baltimore occasionally to railfan.
I sometimes got to the lot on the east side of the tracks on Bush Street off Russell Street. Also near the wye at West Ostend & Warner near M&T (Ravens Stadium).
There are lots of good places in Baltimore, just keep in mind that not all areas are particularly safe. It only takes a block or two to make a difference.
There is also the park by Thomas Viaduct. A 150 year old stone bridge that is still in use. Also, around the corner to downtown Ellicott City, with the old B&O station.
Another good source is:
http://users.erols.com/ttrogers/ He sells some great railfan videos. The Old Mainline #1 starts in Baltimore and goes west to Frederick Junction. The great thing about his videos are that he follows along with a USGS map so you can see the places that he is shooting from.
Happy Railfanning