There was a Strangers and Freaks mission involving Michael and Abigail where you have to collect submarine parts for her underwater (the starting point of the mission is at the Sonar Collections Dock). Michael gets a Dinghy that 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 Merryweather underwater, 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 those Strangers and Freaks missions on you can scuba dive anytime.
I went to the boatyard, and I was able to still find the Dinghy there, and was able to get the scuba gear as soon as I dived into the water from the Dinghy even after completing the Strangers and Freaks missions for Abigail.