1. In virtually all Econ grad programs, the first year students all take the exact same set of classes and comprehensive exams. This happens in very few PolySci programs, to my knowledge. The result is that different sub-fields of Econ share a common language and socialization and communication that I don't see so much in PolySci.
2. PolySci works more to place research in context; more examples, more citations, longer reference lists. Econ is a bit more autistic in that regard.
3. Many political scientists seem to view conference papers as a final goal, where in Econ, they are at best a means to an end. There is little professional reward or recognition in Econ for work that does not get further than conference paper.
4. PolySci is more polite. People speak at length without interruption. Comments at conferences are vague and pleasant. Econ seminars are rude free for alls and comments can be very direct.
5. Polysci is more socially aware. They boycott conference locations due to state or local laws or the presence of non-union labor. I cannot imagine anything like this even being considered in Econ.
6. Econ journal editors are more decisive and autonomous that Polysci journal editors. Polysci usually uses more referees per paper, and it seems to me that editors have a bit less discretion than in Econ.
It may be presumptuous of me, an economist, to write this list, but I've published in Polysci journals, presented and commented at Polysci conferences, even spent a year visiting in a high quality Polysci department (Duke) and another visiting at Caltech which has economists, political scientists and historians all under one divisional roof (or at least they did when I was there).