There was a strangers and freaks mission involving Michael and Abigail where you have to collect submarine parts for her under water (the starting point of the mission is at the Sonar collections Dock). Michael gets a Dinghy which is right next to the Submersible on the Sonar collections Dock when he is on that Dinghy he can drive to those destinations and scuba dive inside the water to collect the submarine parts, basically you have to collect 30 of these parts to finish that Strangers and freaks mission.
On collecting these submarine parts i even found the part where Trevor sinks that weapons cargo plane from merry weather under water and i found lots of weapons and ammo in that area.
I never tried going on the Dinghy after that mission but i think you can still use that to scuba dive any time, also that mission to collect 30 submarine parts wasn't sequential it was like collecting nuclear waste you can resume it any time, as long as you kick that strangers and missions on you can scuba dive anytime.
EDIT: I went to the boat yard and I was able to still find the Dinghy there and was able to get the scuba gear as soon as i dived into water from the Dinghy even after completing the strangers and freaks missions for Abigail.