Stay with the Sapphire Beach Resort & Marina condo options, your TA is giving bad info there. Yes the restaurant and pool bar have been closed for several years but the property is nice. The condo building exteriors have been and are being renovated and there are other improvements planned.
We rent through an owner who lives there and rents 3 condos which are gorgeous units. Nothing beats looking out at the water and islands from their 2nd floor balconies and being that close to the water at night. Another owner has a very nice 2-story if you want more room. But the normal studio is very roomy. Always rent through the owner since every condo is different, VRBO is a good option. If you want owner contact info I can give you our contact too.
Sapphire Village is a less expensive option because you're on the hill behind the marina, but some units offer great views and you're close to the beach. Just not waterfront, and it can be a vigorous walk back up for some.
Bolongo Bay Resort is what I would caution you on in regards to the rooms.
Enjoy your visit!