Phandalin's Tessendar Manor was taken over by my PCs as well.
Leilon seems to be rebuilding from being destroyed in the 4e/5e transition. This would be a good place since it sits between Neverwinter and Waterdeep. You could also build closer to one of these cities, but the lords of either may want to have a say in who lives a day or two from them. This could lead to some good roleplaying though.
You could also have a location that is of strategic value or mineral value. A mountain pass, bridge crossing, or even a well of spring water are good strategic locations. Mines, lumber, cropland, and even coal beds are mineral rich and worth securing. Some of these are rather boring and not exciting to a PC or player to want to be the lord over. You can also combine the two for something better.
Cragmere castle from LMoP could be repaired and make a good home. It has a good location between the main road along the coast and the Triboar trail which should be on the up since Phandalin became more important. It has plenty of lumber to export and can cater to merchants along the roads.
You could also take over Iniarv's Tower next to the Mere of Dead Men, south of Leilon. It will provide a safe place along the trade road and has access to the swamp and mountains, each of which could have resources such as medicinal plants from the swamp or a silver mine in the mountains. The location can also be a good place for adventurers to use as a base while investigatin the swamp. This was done in the 2e time in a Dungeon path, but the tower was just a campsite.