I just finished the whole Stormcloak questline and I am wondering If I could finish the Main questline after the Stormcloaks. I am at the point where I still need to find Esbern at the Blades questline. So Can I? Thanks
You can go through the entire Main Quest no matter which side you pick.
How far you have completed the Civil War Quests will affect some conversation choices. But even after you have negotiated a truce, the war will continue. Some achievements could be affected if you take over a hold tied to one.
Remember, you will have to finish the entire Main Quest before continuing with the Civil War after finishing Season Unending
If you finish either side of the civil war questline before the Main Queast, "Season Unending" will not occur at all, as the war is ended and no truce is needed. but if you started "Season Unending" then finished the civil war before completing "Season Unending" The best advice I can give you to check back with Jarl Vignar Greymane to see if he's verdict has changed, or Go to Esbern as instructed and see if it clears up.