Update :
Full Native PostGIS for Npgsql is shceduled to be released with version 3.1. Quote from npgsql.org version 3 release notes.
Major goals for Npgsql 3.1 includes: Full, native PostGIS support (#529)
And for those who want to keep up with the changes. Here is the feature branch conversation. Support for 2D PostGIS is already merged to default.
For Npgsql version 2.x here is my old answer.
I Posted the question in Npgsql Development forum , and got my answer.
NpgSqlPoint type is not yet Supported by EF due to Entity Framework Data type Restriction.
Seems they are still working on this one.