2-3pm is not rush hour in Tokyo. However, many central subway stations in Tokyo require you to climb flights of stairs to enter, exit or transfer lines, which is not much fun with large bags, and while there's usually a single elevator somewhere, this can add a lengthy detour. If you can tell me exactly where you're going, I can try to recommend a least-bad route.
If you've got large bags and/or are unfamiliar with Tokyo, the Limousine bus direct to your hotel is usually the best option, but availability depends on the destination. I'd suggest two other alternatives:
Take the airport train to the nearest major taxi station, then a taxi to your final destination. (This is what I usually do.) A cab from Tokyo Station to most destinations in Chiyoda should be less than 1000 yen.
Ship your bags directly from the airport to your hotel with Takkyubin. This is particularly useful if you're hardcore and plan to go to the office/customer site before your hotel. Same-day delivery for a full-size suitcase is ~2400 yen and the service is extremely reliable (although at 2 PM you will most likely get it delivered the next morning).