I'm in the same boat as the original poster. I live in Charlestown, a peninsula with three entry points - three absolutely horrible traffic ridden bridges which are all long, filled with potholes and debris and have little to no shoulders. But I'm an urban commando and I will take a lane (and ride faster than traffic lol)
The MM Bikeway is fun, it's one of the better MUPs I've ever seen in terms of riding a bike. Just watch out for Saturdays when it's nice, and it'll get way too crowded. You can always head into Boston on the Orange Line from Malden and hop off at North Station to take the Esplanade out to Watertown or hop off the Esplanade thru Harvard Square and hook up with the Minuteman in Cambridge to ride all the way to Bedford.
For hill climbs within an hour of you...
1) Blue Hills - It's only 600 vertical, but it's steep and sustained. It's in Milton, right off of Route 128. If you were to ride there from Malden it would take you through Roxbury and Hyde Park, pretty crappy areas of the city.
2) Wachusett - this entire area is very hilly and is the site of the annual Charles River Wheelmen Climb to the Clouds Century. If you printed out a cue sheet from the 60 mile or 100 mile ride they have just amazing hills the whole way. Wawa is something like 1000 vertical of mostly sustained with a short flat section about half way up. Great views from the top and a real sense of a climb from the switchbacks and It's about 45 minutes to an hour away.
3) Greylock - a real bear. This one is probably closer to 1.5 or 2 hours from Boston.
4) Ascutney - the serious asswhipper. Get into shape for this ride becasue it's freaking tough, really tough with (I think) serious sustained pitches.
5) Washington Auto Road. - not really open to the public except for the famous race and the training ride, this ride will put Alpe d huez to shame! 4700 vertical feet with a maximum pitch of 22% and an average grade of 12%. You really need to be sure that you've got hte proper gearing on your bike before attempting something like this. I think that Tyler Hamilton (TdF hoss, marred by steroid accusations) holds the record for the climb, which offers snow year round and winds commonly sustained in the 40-80mph range. they have the highest recorded sustained wind there at 231 mph. Now that's a headwind!
a great site with all kinds of info for boston related hill climbs. They rate Wachusett a 1 in terms of toughness which i think is underrated, but maybe I'm just a wimp!
http://www.northeastcycling.com/