Hostels in North America are very basic compared with hostels in Australia and it is VERY unusual for a hostel over there (especially a big city hostel) to offer a pick up service.
The subway in New York runs from Penn Station to all the New York hostels (it's safe during daytime). Boston, San Francisco and Washington DC also have very good public transport between the train station and hostels; other cities aren't so well connected but there is usually some sort of transport option such as a local bus.
Bed bugs are not as common in North America (they prefer warmer climates hence the proliferation of bed bugs in places like Airlie Beach and Cairns), however I have had reports of bed bugs in New York hostels so it is possible that you could get bitten.
Permethrin is considered the most effective insecticide against bed bugs. However permethrin is not a repellant that you can apply to your body and rather an insecticide that is used to treat bedding to prevent bed bugs from occuring. You can buy permethrin-treated sleeping bag liners, which are probably the best protection against bed bugs - although nothing is a 100% deterrent (how often have you covered yourself with insect repellent only to still be bitten by mosquitoes).
Here is more information on permethrin-treated sleeping bag liners:
http://www.travelgear.com.au/mm5/mer...gory_Code=BBUG
Here is more information on bed bugs:
http://www.bug.co.uk/essentials/bedbug.html