There are atleast 7 places to level up at the end of the game, there is actually only 7 I think.

Giruvegan Great Crystal
Pharos Subterra
Henne Mines Extension
Lhusu Mines Extension
- These four places have the highest level enemies

Necrohol of Nabudis
Nabreus Deadlands
- The enemies are a step lower but you can beat many of them

Negalmuur auto-leveling method in Stilshrine of Miriam
- This is an auto-leveling trick where you find Negalmuur, he summons Ghasts, you kill the Ghasts automatically. You stay alive and healthy and repeatedly and easily kill the Ghasts. You have to set up the gambits in a certain way. I'll post a thread on this. Basically you set up the process, it does it automatically and you leave for hours, you come back later and see that the party levelled up for you! You can leave it running and go up to level 99! I get like 328 exp every 11.5 seconds but I can double that with an Embroidered Tippet. You have to set up the gambits right.

I prefer Negalmuur, since it does the work for me, I'll get up to level 99 with little work.