Having 5 days and being anyway in 2 places, I'd try to visit both of them. I'd stay 2 days in ZRH and 3 days in Paris as you mention in your 1st option. 1st day to visit the town of Zurich and on Sunday do an excursion to some mountains nearby, mybe Lucerne and up to Pilatus (theoretically you can go everywhere in Switzerland on a 1day trip, but why go far, if you don't know the places nearby). 3 days in Paris is not a lot, but sufficient to see the main sites.

Forget about night trains, take either the early morning TGV on Monday arriving before noon in downtown Paris or take the late evening flight on Sunday giving you really 3 full days in Paris (or early morning flight on Monday arriving in downtown Paris around 10:00 am depending on traffic).