Running is a great place to start! If you're new to running, the Couch to 5k program was great. I started it when my youngest was 4 months old, and it has been a lifesaver in terms of helping me get back to my pre-pregnancy weight, and now I have more energy to handle my kids (and I only have two!).
I have found that I need to do some strength training and abs work in addition to running to get more toned... I do ten minutes three times a week using videos and a variety of exercises that use my own body weight so I can do them at home.
I've heard great things about cross fit, and I am sure that there are great personal trainers at gyms, too, but for me it's hard enough to get my runs in let alone schedule babysitting time in order to do other workouts. Doing a little bit a few times a week and then running has been manageable for me and I have noticed a big difference.
Think about your schedule and what you can do, start slowly enough with whatever plan you enjoy so that you don't get injured or burned out, and good luck!