I've had a Lager for about 5 years. Never had a problem with it. Easy enough to put a rack and mudguards/fenders on if you wish. I'm sure the Fuji is a fine bike as well.
Regarding shops, I've used Brotures in Kichijoji for bits and pieces. There is a guy there who speaks really good English. They have quite a few fixed bikes in stock.
Close by is a place called Velocraft. Mainly classic type touring bikes, Panasonic, Raleigh, Bromptons etc but also shelves of quality parts (think hubs, brakes etc) if you want to build up something. Not cheap but you will get good service.
In between these two shop is CWS. They have a great range of bikes, mainly road, mtb and decent commuter bikes. Not a bad place for tyres, lights etc.
Now, more importantly. Close to Brotures is one of my favourite ramen shops. Worth the trip to Kichijoji alone.