Whether LFE is better than line in or the other way around depends upon the AVR and overall SINAD (signal to noise and distortion) performance of the chain. Without a lot more knowledge it is impossible to say which is better in any given case. IMO it does not really matter but as Brian says try both and see which you like.
The LFE bandwidth also depends upon the AVR's setting. In practice I am not sure there is much LFE content above 80 Hz; anecdotal evidence from various posts on this site lead me to suspect not much. My very brief trials a few years ago indicated that, for me, rolling off the LFE above 80 Hz did not change the sound noticeably (i.e. I did not notice the change on the few scenes I checked). But, I do not know. If the AVR sends all LFE bandwidth to the subwoofer channel and you roll it off in the sub, then yes that half-octave is lost (note that it will be rolled off over 80 Hz, it does not get chopped off right at 80 Hz). If the AVR is set to roll off the sub at 80 Hz, it depends upon how the AVR handles the LFE content. Again without direct measurements of my own, what little research I have done and reading here on AVS seems to indicate some AVRs redirect the LFE (along with other bass content) above the crossover to the L/R speakers, while other do simply roll it off. Again I do not know for sure. Almost all the diagrams I could find all showed LFE going only to the subwoofer and not to the mains. Some AVRs use a global low-pass setting that rolls off the LFE channel along with the mains; others use a separate LPF for the LFE signal.
As I said, for me the difference between line in and LFE in was not noticeable so, if you are concerned about the higher-frequency LFE content, use the LFE input. Better yet try them both and report what you find. I'd be curious if your findings are the same as mine; I honestly do not know what others might find.
"After silence, that which best expresses the inexpressible, is music" - Aldous Huxley