Does anyone have any knowledge about long term parking options at Zurichs main train station? I am wanting to park my rental car there while I take a train to Lugano for a few days.

Not really that much in Zürich itself. The nearest parkhaus to the HB, the multi storey behind the long distance bus station comes out at 43 CHFs a day. Hardturm is somewhat cheaper but I'm not sure about the area.

You could always park out at the airport, the long stay car park (P60) will cost CHF123 for a week. This might be the best thing as some places have a maximum stay, for instance the one at Jelmoli won't let you stay more than 96h.

Or, since it's a rental car, you could always turn it in and get it out again when you get back.

Can't you hand in your rental & pick up a new one after some days?