We did the Nene this summer, lovely navigation and the few remaining hand wound guillotine gates were OK. As others have noted the main issue is flooding. Based on some very helpful advice from Jim Shead, we moored easily here:
* above the lock in Northampton
* ditto Cogenhoe
* Wellingborough embankment - water point and shopping, not ideal overnight
* above lock at Irthlingborough NB no facilities here at present.
* Thrapston, either above bridge or below the lock (Islip)
* the backwater above Ashton lock
* Fotheringay
* Wansford railway station (steam)
* Ferry meadows, Peterborough
You can just tie up in a field, but I would not recommend it without asking first.
There are no EA elsan points between Northampton and Peterborough. But I rang ahead to the boatyards, who were very helpful.