Three days after Provence cruise

Have you had a look at Google maps? From Lyon it would seem a straight shot from Lyon to Macon, then Beaune, then Dijon. By car they aren't really that far apart. Depending on what you want to do there, you could just stop in Macon for a few hours en route to Beaune. Stay in Beaune . But I'd be tempted to drop the car in Dijon and train to Paris from there, since it will have direct trips with no changes needed. If it was me, I'd be returning to Paris the evening before my flight.

Atexanincarolina,
I would rent a car in Lyon and return it in Dijon as CJean recommends. And stay in Beaune overnight. The Hospice de Beaune is a unique and beautiful place to visit and it is a charming town. And the story of the founding of the hospice is really interesting!

Catch the train for Paris in Dijon (the day before your flight home).
Amusez-vous bien!

Is there an easier way to rent a car in Lyon? The airport seems like a hassle after the cruise and I hear the area around the Lyon train stations are tough. Is there a car rental close to the outskirts of town that might put us on the road to Burgundy easier? Or am I asking too much? We'd like to see Macon and Cluny on our way to Beaune so hate to train to Dijon to get a car and back track. Thank you, friends, for an travel advice.

Take the train from Lyon to Macon, explore Macon, and then take a local bus to Cluny. You may also be able to take a taxi for not too much, and arrange for them to pick you up in Cluny to return to Macon at a specific time. I don't think you need more than 1 day in Macon and Cluny together. Then get back on the train to Beaune, spend the night, and explore Beaune for a day before catching the train to Dijon. With just 3 days though, you may want to choose just two destinations, i.e. Cluny/Macon and then either Beaune or Dijon. If you're sticking to this list, then you don't necessarily need a car, though if you want to get out into the wine villages, then a car rental would be easier. Unless there are significant price differences between renting a car in Lyon or Macon/Beaune, then it would probably be easiest to rent in Lyon. To get back to Paris, take the TGV (buy tickets now) from Dijon to Gare de Lyon or directly to CDG, whichever works best with your return flight.

Renting a car at Perrache station in Lyon puts you right on the A6 motorway. Not a hassle at all IMO.

The Perrache station is close to the mooring point for river cruise boats. Uber or taxi to the station is easy to do from there. We Used Uber and the metro to get around Lyon after our Uniworld cruise last month.