Jax, I would highly recommend the Hoian Beach Resort to stay at Hoian. Its a few k's out of town, but plenty of free shuttles or cyclos. I stayed there 2 years ago and loved it - very classy and relaxing, near beach and river. Probably about 4 star and quite cheap also.
Cant recommend where we stayed in Hanoi, cos it wasnt that nice! It was one of the Hong Ngoc Hotels (theres a few of them). Id say it would be about 2 star, in the "old quarter". As Bob Mac mentions, staying in the old quarter is a real wake up call, but worth it just for the experience! We also did Halong Bay, and apart from the freezing weather, it was great. We did an overnite junk cruise - it was amazing. Cant remember the name of the company we did the o/nite cruise with cos it was all inclusive in our package, but I can find out for you if you want. Its worth doing.

I am SOOOOOOOOOOOOO envious of your trip - so much to do and see!!!! One day (when Ive retired!) I will do trips like yours!!

Have fun! Might see you in Phuket - we are there 2nd-12th April. Look out for 6 aussies (2 mums, 1 dad and 3 kids!)

Kitty