#1 is correct if you use the word "are." The plural form is used because the actual word it is referring to is "kilometers."
#2 is also correct, although in my personal opinion it would be better to say "There is a peach forest, over six kilometers in size, in the village."
There is a small difference in meaning. If the village contained three separate tracts of peach forest, with a total area of over six square kilometers, then #1 would be correct, but #2 would not be correct. "Forest" can be a countable noun for an unbroken wooded area, or an uncountable noun for "wooded land."
Usually, small integer numbers are usually written out in words rather than numerals. Authorities differ on "how small is small." Some say to spell out from one to ten, some say one to twenty, some say one to a hundred.
Finally, another unit of area is the "hectare." A square kilometer is 100 hectares. I don't know the rules or customs regarding which to use in a case like yours.