There is a remarkably common problem with Jetta heater boxes. I have discovered it in my own 2003. When we purchased the car used we noticed a flurry of foam from the vents when heat or A/C was turned on, and thought not much of it. I just figured it was probably a lining of some vent that had worn over time. Since that time...with extremely poor heater performance my research led me to discover that the vent doors, once sandwiched with foam deteriorate over time and leave stamped metal doors with huge holes punched in them. These now obvious holes leave hot air to mix with outside air, and never divert hot air as they would if they were solid.
Since a pic...and a very helpful video is worth more than a thousand of my words...check this out if you discover all else recommended has failed. I believe you would want to take a look at this before you go replacing the heater core.
http://www.youtube.com/watch?v=4c1cjA-y7yE