The municipal Gyms are a cheapo's friend!
For other cheaper ideas, doing a Japanese martial art might be an interesting experience. Aikido and Karate aren't as trendy in Tokyo as Yoga, pilates and cross fit, so they tend to be much cheaper.
I'm a fairly heavy gym user and I like to go early so I joined a commercial gym - Gold's gym. I chose it because the day time plan isn't so pricey, the facilities are great, they have kettle bells and large studio spaces that are usually unused outside of the class schedule. There's also Anytime fitness, there's a lot of those around Tokyo, they are cheaper and open most hours.
On an amusing side note, I've noticed recently in a couple of parks around about 6:30am a load of pensioners doing "ラジオ体操" - radio taiso, the radio excersizes. I believe this is the NHK Radio Taiso schedule if you fancy tuning in and joining at home
Bonus points for practicing with Youtube first https://www.youtube.com/watch?v=xS92XkVKM0Q