I tend to stick with the Red Rocket with no settlers allowed. Keeps them from taking my stuff.
However I am leaning towards Greygarden for later in the game. The robots don't use weapons so they will not raid my collection when an attack happens. Plus they don't sleep so I won't find them in my bed when I want to take a nap. Another bonus is Supervisor Green, he happens to be a merchant, so I don't have to run to town to sell off my junk items.
I'm not a fan of building on the highway over passes so I will probably have to spend some time leveling out the slope with foundation blocks and building on top of them.
The only real drawback of Greygarden is the lack of open water to build Water Purifiers on. But having a robotic merchant on hand cancels that out as far as I am concerned. I can get Purified Water from another settlement.
A few other settlements have merchants living on them but your back to the issue of human/ghoul settlers stealing your weapons and sleeping in your bed.
For those wanting some place already built you do have a few options. There is Home Plate in Diamond City. You can decorate it to suite your tastes. Another is a room in Vault 81 that you get after doing a few quests. It has a bed and storage for your gear. The biggest draw back to these is no crafting workbenches for your gear in either place. Diamond City is a bit better with workbenches just outside. But, you have to haul your crafting supplies outside when you want to craft anything.
Finally, you can take any of the settlements and use it for just yourself if you choose to. You just have to kill off any settlers that are there before you. Just don't have any companions with you when you do it. Most get upset when you kill settlers.
If I could pick any spot on the map I would take the Atom Cats base. Assuming I could clean up and get rid of the junk yard its set in. Red Rocket building as my home and the big barn as my workshop and Armory for my Power Armor. Some foundation block walls with turrets and you have home sweet home.