Unless you or a previous owner has put dirt in the cooling system, your heater core should be just fine.
I bet the louvers are hanging shut inside the heater box. Or, the T-stat is not functioning properly .... thus, engine is running well below normal!
2000 Jetta, 350k miles
'84 Vanagon ALH TDI engine (35+ MPGs consistently) Malone Stage 1 tune. Road trip to Alaska summer '14, 11k miles round trip
VWs 41 years, VW diesels 34 years, ALH TDIs 12 years.