Gringo: you sound like a wonderful guy for wanting to do somethng special for your hunnie!!! What a great catch she caught!
I too spent my honeymoon there in San Pedro. The most wonderful time we had were the romantic dinners with lots of wine and sitting right next to a window looking out at the ocean. There is a place up North, although they don't have the window, that has great food and great wine. Whew, forgot the name and had to look it up (on this site), it's called Mambo Restaurant and it's at Mata Chica resort way up North. The ambiance is great - have them seat you in what I think is the lobby - for a glass or 2 of wine before dinner. You can purchase a cigar right there, if that is what pleases you.... It will be a wonderful night. Warning: it is a bit pricey. You can look under lodging on this site and click on Mata Chica to check it out. A water taxi will take you there. Check them out at Fido's pier.
Good luck and I am sure whatever you do will be great; your bride surely knows what a great guy she has.