If you change y to a data.frame you can add some 'jitter' and with the col option you can set the transparency level (the 4th number in rgb):
y <- data.frame(y)
pairs(sapply(y,jitter), col = rgb(0,0,0,.2))
Or you could use ggplot2's plotmatrix:
library(ggplot2)
plotmatrix(y) + geom_jitter(alpha = .2)
Edit: Since plotmatrix in ggplot2 is deprecated use ggpairs (GGally package mentioned in @hadley's comment above)
library(GGally)
ggpairs(y, lower = list(params = c(alpha = .2, position = "jitter")))