There are a bunch of marinas along the waterfront in Lisbon. I dont know them well enough to recommend one, but all are close to different areas of town. I suggest researching the neighborhoods to see which you would prefer.
Public transportation is very good, plus there is Uber and taxis.
Crime rate is low in Lisbon so I doubt security will be an issue in any of the marinas.
Admittedly it was a few years ago but we found the centre of Lisbon very hot and airless so we dropped backdown river to Cascais which was must more pleasant and the train service from there to the city was excellent
There is Cascais, then one just past the bridge who's name I cannot remember.. as for the rest, you have no chance.
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We stayed in Oeiras marina and were very happy there. Good facilities and staff. A train runs every 30 minutes to take you to the heart of Lisbon. The train took about 15 minutes and was cheap.
The marina delivers fresh bread to your boat every morning, complimentary. The cost was much cheaper than Cascais.
We used the one in Cascais, just before entering the river. There is a fast and moderately priced train to Lisbon from Cascais every about 40 minutes or so.
Cascais is not stellar either but I liked it way above Lisbon.