Each program has it's advantages. Bithacker is amazing because you can draw so quickly in it, and it has the ability to display multiple bytes side by side. It makes hacking stuff like this a snap!
HOM3 is awesome because it has so many features like the TIA pallete, searches that can do strings of bytes, the ability to pin comments, etc... I use HOM3 a lot when I'm not disassembling a game.
Stella also now has the ability to directly hack graphics. Just click the ~ key to enter the debugger and scroll until you find the graphics. Stella will disassemble the rom into code, and graphics sections which help a lot! Stella will also distinguish between graphics constructed with the playfield vs graphics constructed with the higher resolution player registers. Stella's huge advantage is it continually disassembles the rom as new areas of the game program are reached. This really helps in identifying which parts of the code may not be used, etc...