Maybe you could do something like this. To read the data, use the fill argument in read.table. Where text = txt, you would put your file name there.
(dat <- read.table(text = txt, header = TRUE, fill = TRUE))
#   LA NY MA
# 1  1  2  3
# 2  4  5  6
# 3  3  5 NA
# 4  4 NA NA
Then we can take the column means and create a new two column data frame.
cm <- colMeans(dat, na.rm = TRUE)
data.frame(state = names(cm), mean = unname(cm))
#   state mean
# 1    LA  3.0
# 2    NY  4.0
# 3    MA  4.5
where txt is
txt <- "LA NY MA
1 2 3
4 5 6
3 5
4"