Nether are great choice given the time of the day, but HND is far closer to Shinjuku. Just some delay on arrival flight then choices of transport to Shinjuku can be very limited that time of the evening. But I think from HND you will have better options of getting to Shinjuku if a flight was delayed for one hour. Remember, public transport trains and buses do not run 24 hrs. in Tokyo.
If choice is NRT then will you consider lodging right near NRT for the first night, which is cheaper comparing similar level hotels at Shinjuku? At that time of the day I really do not think you will do anything but just crashing on a bed after arriving at Shinjuku. If so then why not just get a hotel near NRT and head to Shinjuku first thing next morning?
If considering simply cost of getting to Shinjuku then from HND will be cheaper because HND is far more closer to Shinjuku then NRT.