Been to both, was actually in Hilton Head this past summer. Myrtle beach has more shuls and when I went, they had one kosher restaurant that was really good but expensive. I think the friendlys ice cream and Krispy Cream had hashgachas; not sure if they still do, this was 6 years ago. Hilton head chabad delivered dinner to me every night I was there, food was fantastic. Do not have local daily minyanim. Myrtle beach has small kosher sections in their supermarkets too. Myrtle beach is also simpler to navigate around, and if you fly to their airport, then everything else is close by. Hilton head's local airport usually requires a stopover in ATL, otherwise you need to fly to Savannah and drive roughly an hour.
Savannah is a very nice city to visit. Hilton Head also has really nice resorts. Myrtle beach is more of a strip of hotels on the beach, though a lot of them are very nice.
Hope this was helpful
