My husband and I will be spending 5 and half days in Lisbon with our 3 year old boy.
Here are what we are thinking to do:

Day 1 and 2: just wondering in the
city
Day 3: Parque das Nacoes (Monday)
Day 4: Sintra (Tuesday)
Day 5: ??

Any ideas what to see and do with our boy for the rest of our stay?

After Lisbon, we will drive to Evora and spend 3 nights there before going to the Algarve (Lagos).

A few years ago we went to Portugal with our children, and our son was 4. He did just fine, and so did we Things he enjoyed were the castle San George in Lisbon, the little beach in Cascais, The Boca in Cascais, and the old castle is Sintra. We stayed for a few days in Lisbon and then a few days in Cascais. The Cascais hotel had a pool which was good for the kids as well. Sort of a change of pace.

The castel San George would be tops on my list, especially if you can still take the old wooden trolley car (forget the number) to reach it.

I think a little boy might also enjoy riding some of the simple funicular trains around town, as well as the elevator San Justa.

You can take a regular commuter-type ferry across the river from Lisbon and back again, and the light rail that runs out to Belem might also be fun, just for the novelty of the ride.

Once in Belem, the tower is an obvious choice, but make sure to make time for custard tarts at Pasteis de Belem. Something else your little boy might enjoy in Belem is the Carriage Museum.

Have a good time (and let us know how it went!)