Hi Holly...and Congratulations on your upcoming wedding as well!
Let me start with the premise of you wanting "a relatively relaxed trip to Portugal" and go from there. You can accommodate some beach time as well in Sao Miguel, Azores. And remember, both of you know your stamina and interests and travel abilities as none of us do.
With 2 weeks, and assuming you will be flying out and back to Boston, then SATA airlines is your best choice. I will say more about SATA towards the end of this post. You can fit a few days in the Azores and I would do it if you like my ideas and of course Rick's recommendations for the mainland, but for me I would leave the best for last..Sao Miguel.
My 2 week plan...fly direct to Lisbon but do not rent a car yet until leaving Lisbon. Do what is in the book for Lisbon, but there are many choices you need to pick from. The 3 Lisbon walks- allow a full day. Belem at an enjoyable pace- another day. Sintra- another full day. Another couple of days is great for Lisbon. When ready to go north, get the rental car. Skip the Algarve and the beaches to save for another trip in conjunction with Spain ;-) Visit Obidos for 2 hours and walk the wall (add an hour), Alcobaca about 1 hour (buy cork products at one of the stalls/stores you see here, the prices are the best in Portugal and the workmanship is very high quality), Batalha-1 hour, drive through Nazare...and I really liked the views from Sitio-1 hour. Fatima, if you are Catholic, can be seen in a couple of hours on this day as well, as the towns are really close to each other. End this day in Coimbra and stay 2 nights. A full day is a must for Coimbra. After Coimbra head to Porto. A full day just for Porto was good, another full day to drive the Douro valley was enough as well. Fly to Sao Miguel. This leaves 4 days for Sao Miguel Azores.
Read the websites for the Azores, watch youtube videos, look at photos... there are many beautiful beaches here instead of the Algarve for this trip, Vila Franca do Campo, Populo, Ribeira Grande will allow you your beach time. 3-4 days for Sao Miguel can provide a lot...with a car! Very easy to navigate around an island to see the highlights. Pick a hotel in Ponta Delgada (preferably with free parking), then go see Sete Cidades, backtrack to the Pineapple greenhouses and on to Vila Franca do Campo and Furnas village where you must have dinner where the restaurant cooks the meal in the earth using geo-thermal heat. Another day quickly visit Ribeira Grande then off to the Nordeste, by the windy coastal road, not the highway! Visit the tea plantation and stop off at every Miradour (scenic lookout and each is unique) and have a picnic lunch at one of them (get your wine and food at any market). Savor the beauty of this gem of a destination and the clean ocean air and the majestic hills and mountains and the grazing animals everywhere! Continue your drive to Povoacao then back to Ponta Delgada. Ponta Delgada is simply stunning at night wandering around the streets and the port area and sitting at an outdoor cafe thinking of your next trip to Europe.
Here is where you have to figure your flights. Try a multi-stop itinerary on SATA from Boston-Lisbon then Porto-Ponta Delgada-Boston using your specific dates. If the price is what you expect, book it on the one ticket. The flight from Porto to Ponta Delgada may have a quick stop in Lisbon or Terceira. Another option, Boston to Lisbon and then Ponta Delgada to Boston on SATA, but book Ryanair for the flight from Porto to Ponta Deldada. If the cost for the flight from Porto to Ponta Delgada is a couple of hundred bucks cheaper flying Ryanair, I would do it. Just make sure you read the about the fees associated with the different ticket options Ryanair offers and purchase the one you prefer. SATA offers different tickets as well with different prices, one with just a carry-on...read the rules!!!
Hope this helps...Boa Sorte! Good Luck!