One good way to get some of your exercise in is after each pomodoro, for your break, do 50 jumping jacks as fast as you can, and then sit right back done and start another pomo. I've started switching it up and doing 10 pushups as fast as I can instead, and eventually want to work in situps. The key for me is to not have a pomo going while deciding what my priority is, checking email, or getting ready to work on a specific thing. Then in order to get the maximum productivity out of myself I decide on a goal which is a piece of my current priority project, which will take between 3-5 pomos. Any less than that and I lose productivity, any more and it is not as fun because I get worn out and have to take a longer break in between. After I complete my goal, I take a real break where I do something that involves my other senses and relaxes my brain. For example I might take the dog out to go potty, or wash a few dishes, or brush my teeth, or get dressed for the day. If you work from home you can try out starting work in your pajamas and then start getting showered and dressed and stuff on your breaks.
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