The swim cannot be substituted for the run on the CFA. In fact, while at USNA, you must do the run. When I was in the USN (not USNA), you could swim 500m vs. run 1 mile. Now they do 1.5 miles and I don't know if you can still substitute the swim. But that won't apply until you graduate.
If you pass the CFA at NASS, you're done. If you think you can substantially improve your scores, you can retake the CFA and submit new scores. If you fail the CFA at NASS, you will need to retake it and pass to secure an appointment.
Bottom line: you will be much happier and more successful at NASS if you show up in reasonable shape. There's still 6 weeks or so to improve your level of fitness if you think you need to -- use it!