Japan is a cash society.  Luckily, it is the safest country in the world so it's okay to carry large amounts of cash with you at all times without the worry of being mugged or held up.  Generally there is no need to buy Japanese yen in your home country before your trip, as you will most likely pay a higher commission (about 3%) and a worse exchange rate than you would get at the airports, banks, or ATMs in Japan.

There are three ways to obtain yen in Japan for approximately 1% cost.  The first way is to exchange travelers checks (in well-known currencies such as dollars, euros, pounds, etc.) at a foreign exchange counter at a bank.  International airports also have these counters just outside of immigration inside of the arrivals lobbies. Bring a large book if you go to a bank, they have pages of forms and four or five people who need to approve everything. Larger hotels in all big cities and many medium and small cities will have an "exchange desk." They use the same rates as banks, and some days like Sunday, if open you can "win" because they go on the 'closing' Friday or Saturday. They are much faster because a single clerk does the whole transaction.

If you are changing cash, you frequently get a better rate at certain airport counters because they hold and trade that same cash out, but in inside the country the spread on cash is 3 to 4%.

The second way to obtain yen for a 1% fee is via a post office ATM, using a Visa Delta/Cirrus/Plus card.  These are available in most (maybe all) Post Offices. They are often accessible in a foyer even when the Post Office is closed. See this link for more information. Japan Post ATMs have an English option on the menu once you insert your card. Foreign cards are acceptable in 7-11 ATMs too.   Also Narita arrivals hall has a Japan Post ATM. Effective June 20, 2016, single transaction withdrawal limits from these machines is JPY 50,000.

The third way is to find a JUSCO store (big grocery and department store all in one).  There are several money exchange machines (dollars to yen) just inside on the first floor.  You get the going rate for yen and all you have to do is feed your dollars in and yen comes out.  You can change anything from $20 up.

Hint: Many machines issue bills of 1,000 and 10,000 yen. If you prefer to have some smaller bills, withdraw an amount such as 19,000 Y for 9 x 1,000 Y notes instead of 2 x 10,000 notes by withdrawing 20,000 Y. Breaking a large bill for a small amounts does not seem to be a problem in Japan though - most merchants carry plenty of change.

Credit cards are accepted at major hotels and larger restaurants.  Small business hotels and small restaurants generally do not accept credit cards.  The credit card company will charge a fee on your bill for foreign exchange (usually 1-3%), and there may be a surcharge from the retailer/hotel to pay by credit card - ask first. 

Foreign currency and foreign travelers checks are not accepted anywhere in Japan except on certain U.S. military bases and facilities.