Yes, there are other places also on the island apart from the capital town where you can enjoy this mesmerising boat ride. Elephant Beach in Havelock Island (now known as Swaraj Dweep) is a good choice. This beach is one of the most frequented beaches in the Andamans and here, you can hop onto the glass-bottom boat to see the colorful corals.
In Neil Island (Shaheed Dweep), Bharatpur Beach is the place where you can avail a glass-bottom boat ride. It is a very popular water activity there.