I don't know your wife, so she may be just fine with a "lodge" setting, but often times a "lodge" is too one dimesional for someone who isn't all about hard core fishing all day, every day. I have found most spouses are happier staying at a place with more resort amenities and hiring out guides or DIY for the fishing. If you are looking to mix a few days bonefishing in with more typical honeymoon activities I have a few ideas for you in the Bahamas that should fit a mid-range budget.
Long Island - Three resorts I'd recommend in order of cost and service level (highest to lowest) - Cape Santa Maria, Stella Maris, Chez Pierre. For guides I would contact Dockey Smith or Loxley Cartright.
Grand Bahama - There are several nice properties in the Lucaya development and for guides H2O bonefishing, or Pinder brothers.
Exuma - Stay at Sandals Emerald Bay (this is a traditional "honeymoon" resort, also very expensive). There are good flats in the area but I don't have any guide recommendations.
Have fun!