Do I understand right that the component is still in the board, with the solder in the holes?
I've never been a fan of vacuum desolder gear, only owned a cheap one myself and used a few Weller and pace ones at various places of work -- never had any particular success with any -- couldn't say whether the older pro ones were losing their suck and the cheap one was just rubbish, always kept filters clean etc but never found them any more effective than solder wick and flux or a descent long-travel desolder pump.
Is the LED by any chance connected to an internal ground plane without thermal relief, that's a big cause of trapped solder and difficult to remove THT parts. In that case, you may find it a little more beneficial to heat the board with hot air, not quite to melting or to risk burning the board, but just enough that the board won't totally drain the heat from the soldering iron tip. Using plenty of flux, solder wick, (refilling the joint with fresh solder can help it wick out better) and wiggling the pin as it cools again can help break it free from any remaining solder.