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 TDI, 50+ overall average (no tune)
300k mile mark on 12/28/11
, in Excel spreadsheet, 341k miles...
'84 Vanagon ALH TDI engine (32 mpg) Malone Stage 1 tune, Polaris Diesel ATV, Allegro Bay RV 5.9 cummins,
VWs 41 years, VW diesels 34 years, ALH TDIs 12 years