Ask Mr. Smarty Plants

We can't believe it's still alive, period. If it dies when you transfer it to a pot, it will be because you didn't transfer it three years ago. An agave is a desert plant, it can go into the ground, but at this point, it would be better to get a bag of "cactus mix" potting soil, and get started. Take the agave out of the water, and examine it for portions of root that are NOT rotted. There is no use going to all the trouble of repotting, and putting a rotted root into the soil. You didn't say which agave you have, some of them can get quite large (although not in a vase of water) and most of them have defensive spines and sharp tips. Work with heavy leather gloves. Separate the good portions of the plant that have roots, and put each rooted section into a pot with the cactus mix in it. You can water it so it won't die of shock at being suddenly in dirt, but not too much. 

If you choose to keep the new plant indoors in a pot, the agaves are so slow-growing that you shouldn't have to transplant into a larger pot very often. They can do very very well indoors in a good light from a window. Remember, they are succulents, and like most other succulents, they need less water and can tolerate quite a bit of shade. For more information on container gardening, read this article from the Lady Bird Johnson Wildflower Center "How To Articles".