Understanding that the title of this thread asks for recommendations on iPad nav software, I wanted to add that I recently went through this process myself. I have the "older" iPad Air, WiFi-only model (no cellular Internet).
I downloaded the Navionics app and loved it while playing around with it at home. I thought that I would be able to download charts and at least view them while I was on the water (even if my position was not displayed, as I do not have an external GPS receiver). I was disappointed to say the least.
Instead, I ended up purchasing a small handheld Garmin GPS that is waterproof and floats.

I hemmed and hawed, thinking that the small screen would be a serious detriment to using it. I am happy to report that it is not a factor. Fortunately, while sailing at 25-foot boat, I have plenty of time to look at the little screen.
http://www.amazon.com/Garmin-GPSMAP-Waterproof-Marine-Chartplotter/dp/B003I86PJG/
I was positively *elated* (and relieved) to have had it aboard last weekend, while I was soloing, when I was caught out offshore outside of the entrance to the L.A. Harbor (read: huge container ships passing through) in a fast-moving fog patch. I lost sight of the breakwater while I was perhaps a mile and a half out. What a relief to be able to glance at the GPS to see where the opening in the breakwater was!
Long/short: I arrived at the conclusion that I valued the iPad enough to want to keep it dry and off the boat, and decided to use a purpose-built, waterproof/floating, dedicated handheld unit instead (we also have a Porta-Bote and a tandem kayak that we use this with).
Good luck! Happy sailing.