As far as I know, the the BOM GOA ferry hasn't re-started since it went out of business quite some years' ago. And with the opening of the Konkan railway, it became an obsolete travel option.

Rail takes all day, or all night. If you can park your bags after check-out time at your BOM hotel, the overnight train saves a night's hotel bill. Day time you get rather too long to appreciate the scenery. Goa station options are basically three: in the north for Pernem and Mapusa, serves the northern beach resorts; one in the middle near Panaji (quite the nicest state capital) and the other at Margao - great for beaches like Colva.

Air clearly saves time, and with advent of competition AND low-cost carriers, it's not a high-cost option. On Jet and others you'll be trapped into relatively high non-resident fares, but Air Deccan will sell you INR fares through their website - I paid aound INR2000 one way GOI BOM last time I used them. Air Deccan also do Hyderabad and Bangalore.