Freo is ages from Bunbury. Anyway, my kids like sci tech and the zoo, there's another zoo sort of thing at whiteman park. it's exxy but you can pet and feed kangaroos. there are also tram and train rides at whiteman park, if your kids are like mine and love that sort of thing.
Museum in the city.
There are other little museums around the place - taxidermy, trains, etc
Wine, cheese and chocolate in the swan valley, though if you've done margaret river you can probably give that a miss

Yeah, those motor lodges are a good bet, probably. convenient location and easier getting in and out than in city.