One thing to keep in mind is that Manayunk is still in Philadelphia and Bala Cynwyd is outside of Philadelphia in Montgomery County. Therefore, if you work inside of Philadelphia, you will pay a higher tax rate in Manayunk and a lower tax rate in Bala Cynwyd, essentially giving yourself a slight raise by living outside of the city.
New tax rate: As of January 2008 the Philadelphia resident rate will be 4.219% and the non-resident rate will be 3.7242%." - see web reference
Manayunk appears to be the more "hip" area to live, with many young professionals just out of college - as a recent college graduate, almost everyone I know who moved to Philly took residence in Manayunk.
Bala Cynwyd, although close to St. Joe's, is a more family oriented area. You're at the edge of the main line, and as you travel down Rt 30 into Montgomery County, you venture more into suburbia. Depending upon the part of Bala Cynwyd, you're bordering what is typically viewed as a less safe part of Philadelphia, with City Line Ave separating Bala Cynwyd from Philly. However, a few miles west and you're in the heart of the main line - Narberth, Wynnewood, Ardmore, Haverford, Bryn Mawr, Wayne, etc.