They are both in excellent locations. The Southwark location is one of my favourite areas of London...but transport wise the black friars location is easier to get to with luggage as it is on the district line, so only requires 1 change on the tube from heathrow - change at I think hammersmith and you don't need to deal with any stairs etc.

Premier inn is perfectly fine, we stay at them all the time. The lack charm, but the rooms are modern, basic and clean.

I was going to say much the same as jamikins, but be aware that the "Novotel Blackfriars" is actually on the south side of Blackfriars Bridge, so it's much nearer Southwark tube station.

For Southwark tube station, change at Hammersmith (as jamikins says) to the District Line eastbound (just walk across the platform), then at Westminster to the Jubilee Line eastbound (escalators all the way) to Southwark (escalators and only a few steps to street level).

It's not far from the Premier Inn, as it happens, which is nearer the next tube station along from Southwark (London Bridge), but a few minutes' walk further away from a rather more generous choice of public transport.

http://www.tfl.gov.uk/gettingaround/maps/buses/pdf/southwark-a4-231112.pdf
http://www.tfl.gov.uk/gettingaround/maps/buses/pdf/london-bridge.pdf