I don't know much about boys' clothes, but I did a quick glance through both volumes of The Way They Were
, and found 4 boys (ranging from just-out-skirts to teenage) in pants with a small check pattern. Another had what might have been a narrow stripe or another check, and all the rest were in solid colors. The matching coat/pants combo occurs more often than a contrasting coat and pants (about 28 to 14), and almost all of the buttoned-together shirt/pant suits are of a single fabric (though at least one boy has a contrasting shirt/pant out of this style). There is one boy with a plaid shirt and solid pants (the plaid is the same in as the dress of the girl next to him), and another with a check top and solid bottoms.
It's possible that some of the checks were plaids which washed out when photographed (the dress in my avatar is a plaid in real life, but looks like a check in wet-plate photos because the narrower lines wash out); by a wide margin, though, solids seem to be the most common option.
I did find this plaid suit, but it's for a rather younger boy:http://www.metmuseum.org/Collections/search-the-collections/159177?rpp=60&pg=1&rndkey=20131115&ao=onft=
(the hyperlink doesn't seem to be cooperating, but you can copy & paste the URL).