Hopefully they don't delete this answer, as I have used this answer when I read a previous question a lot like yours. After about a week of research and banging my head against my desk, I FINALLY got my Npgsql MVC Entity Framework application to work... and work WITH the wizard. The steps are below....
1) Close Visual Studio, then download and install Npgsql PostgreSQL Integration from: https://marketplace.visualstudio.com/items?itemName=RojanskyS.NpgsqlPostgreSQLIntegration
2) Reboot your computer. (yes, it's needed, I promise)
3) Open visual studio and install the following NuGet packages, IN THE ORDER listed and the VERSION listed...
--> EntityFramework version 6.0.0, then clean and rebuild
--> Npgsql 3.1.0, then clean and rebuild
--> EntityFramework6.Npgsql 3.1.1, then clean and rebuild
NOTE: You may need to uninstall other Nuget packages if these will not install in the order and version listed. If so, just make note and add them back later. and yes, you will want to clean/rebuild between each one above.
4) Close all applications and restart your computer. (yes, it's needed, I promise)
5) After your computer restarts, open Visual Studio again and go to your solution. NOTE: I advise you add a new project for your database connection, but this is more a preference than anything.
6) Try using the Entity Framework Wizard again. You should see the Npgsql selections and it shouldn't just crash on you.