If you are looking for primary sources in English, there's really not a lot and it's mostly by diplomats.

Commodore Perry's journey itself can be sourced through these books: http://www.digitalbookindex.org/_search/search010hstuscommodoreperryexpeditiona.asp

The story of the British counterpart, Lord Elgin, can be read from Lawrence Oliphaunt's book: Narrative of the Earl of Elgin's Mission to China and Japan. http://books.google.com/books?id=5--b2WGQ9P4C&printsec=frontcover&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false

You can then try Townsend Harris's (the first American consul in Japan) diaries:

https://archive.org/details/completejournalo00harr

The British consul Rutherford Alcock also published a book in 1863 called Capital of the Tycoon

https://archive.org/details/capitaltycoonan02alcogoog

Young Japan by John Black was published in 1880 and is a narrative of Japan after its opening.

https://archive.org/details/youngjapanyokoh00unkngoog

And Ernest Satow, a British translator and later minister to Japan, wrote a memoir called A Diplomat in Japan in 1921. I think there's a book out there that has also compiled his letters.

http://www.gutenberg.org/ebooks/43541

Francis Hall's Japan Through American Eyes, 1859-1866 is the only widely available primary source of the Bakumatsu era from a merchant's point of view.

Black and Satow cover the Boshin War.

Beyond that I would use the standard stuff, such as newspaper articles from the time (both the New York Times and the Times in London were reporting the war), US state department archives and UK foreign office archives or parliamentary papers.

If you can read Dutch W H van Kattendijke wrote a memoir of his times teaching naval skills to Japanese samurai and Dr Pompe van Meerdervoort wrote a memoir about his time teaching medicine in Nagasaki.

If you can read German I suggest looking at Siebold's writings (both father, Philip and son, Alexander).

Also Edouard Suenson, a Danish guy working for the French navy, wrote a memoir of his time in Japan.

If you can read Japanese then your have tons of primary sources (and most of the stuff above is translated into Japanese as well).