We have just done what you are anticipating (but from high desert of Oregon- very limited sailing opportunities there!). We looked at both Punta Gorda and the general Cape Coral/ Ft Myers area. We decided on CC for several reasons but primarily it seemed like there was more to do (other than sailing) and better/ more convenient flight connections.
If those don't matter for you, then definitely consider Punta Gorda as the sailing area is more convenient. In general, the homes will be a little bit less expensive in PG.
For Cape Coral I would look harder in the SW region (that's where I live). We looked all over before deciding and the reasons we decide that part is multifold. First you can shave maybe as much as one hour off the transit time to more open water. Definitely look at the charts. A lot of the water you see in the river is so shallow you can walk most of it with your head out of the water. Homes off the river will be a bit less expensive than the lower part of CC partly for this reason. You might consider the NW part (north of Pine Island Road) of CC which will take you to Charlotte/ Punta Gorda sailing territory. There is a lot of skinny water between the Pine Island Bridge/ Matlacha canal that leads to those homes and up to sailing territory. We were told that during the low water time (Feb ) it is very shallow (barely 4 ft) going over the oyster bars to get out to the channel. I have seen sailboats (few and far between, though) behind homes in NW section. Other things to consider about the NW is that most are on wells/ septic systems and the city will eventually force you to hook up to water/sewer system that will be extended to that area. You can count on that costing you over $20K, so factor it into any offer you may make. Also the city/ county whats to increase the size of burnt store rd to up to 6 lanes. Some properties on Burnt Store road are involved in imminent domain fights mostly on the value the gov wants to pay for the property. That's a very real issue as being on the West side of Burnt Store road would offer some of the most convenient sailboat locations, but ultimately the gov will win. They'll have to pay more, so it may take longer.
For the SE/ SW area (called the Yacht Club area) it is getting very difficult to find Sailboat access for under $400K (and that property will likely need 50-100k in remodeling.) The very eastern -southern bottom part of CC is the original section of town. You can find a lot of modest small homes in this region along with newer properties that were rebuilds after tearing down the original homes. A given street can have quite a mix of homes. Most of the canals are 80 ft wide. One option to mention is that there are publicly available slips at the "Yacht Club". I think for city residents the rates are reasonable (under $10/ ft/ month) but double check as the rates may have changed.
In the most southern and westward section of CC you can find homes, some on 200' wide canals. There is a lock at Cape Harbor that you may need to factor into transit time. Homes in this area tend to be newer by say 20 years than the Yacht Club area.
If you need a recommendation on a truly excellent realtor, I can provide you a reference.
