Definately silicone is the sealant of choice. I would make a recess in the tank, in which the glass sits. Depending on the size of the window allow for more or less caulk thickness (up to 1/2" on a large window). This to allow for differences in expansion. Make the inside flush. I would suggest a 4 or 5 mm seam around the perimeter, and some 3mm on the bondline.
Make sure you meticulously clean the bonding surfaces. This is where 99% of the problems start. degrease with water and ammonia, then do not touch the mating surfaces anymore. Tape where the silicone should not go (the edges of the recess, interior and exterior, the edge of the glass, etc). Apply a generous bead on the mating surface, and stick some distance pieces in, which can be removed later. (this ensures the right bead thickness). Press in the window, and fixate. Now clean up the mess on the people-side. Apply more sealant on the fish side to fill the perimeter, and clean up. Remove the distance pieces, rework, and you are done.