Just got back from a week in Portugal myself. Where are you staying? We've been there several times due to family connections and have stayed in various hotels. The Portuguese do love children but don't necessarily have baby equipment ie high chairs and baby changers in toilets etc. Consequently I always take a baby harness thing for 'tying' the kids to chairs during meal times. They fold down to nothing so are well worth carrying around. If you have room you could always take a portable high chair.
Are you hiring a car? We also always take our own car seats (although you can usually hire these - but book in advance). Even if you are not and are just transfering from airport to resort in a coach you may want to take one with you. The Portuguese aren't renown for their conscientious driving....In fact the road from Faro airport to Lagos is one of the most dangerous in Europe. Also useful to take the roller sunshades that go on car windows.
Ditto on the small paddling pool. Especially if you are heading for the beach. The sea around portugal can be very rough. However, mine love the beach. It's a giant sand pit to them!
If you head for the beach you'll need some shade...I usually take our ELC pop up tent. It provides some shade, a place for storage on the beach and folds flat (although hubbie hasn't mastered that bit yet!). You'll need lots of sun tan lotion and sun hats etc. I got a burnt back last week whilst sitting on the beach during a cloudy morning...Should have known better.
An excellent toy to take is a stack of plastic beakers....the kind that stack on top of each other or slip inside each other (so packing small). They make excellent bath and beach toys.
You can get pampers and baby food etc at the local supermarkets so you don't have to lug a pile out with you.
If you are flying to Faro (I'm kinda assuming you're heading for the Algarve)....there is a small play area in the departures lounge. Nothing special but enough to pass a few minutes and burn off some energy. Also they have a toy shop that has some lego on display to play with. A top tip is to slip some bubbles in your changing bag. Excellent entertainment if you get stuck.....
Hopefully your son will be nice and steady by September as a lot of Portuguese accomodation comes with tiled floors....Nightmare. Been there and don't want to repeat that...
Oh, another thing you might like to try if your boy is a good sleeper....We normally take our baby monitor with us. Once the boys are asleep (an provided it's in range) we can take it down to the bar for a quick coffee (!) knowing we can hear if they wake up. You'll need a travel adaptor though unless yours is battery powered.
I'll let you know if I think of anything else.