Miyamoto has been at Nintendo since 1977, with Genyo retiring he is the oldest senior level employees there.
What about Makoto Kanoh? Joined in 1972 as well, seems to be in semi-retirement since mid 1990's but still appears here and there.
Takehiro Izushi, who joined in 1975, definitely retired I think.
Takao Sawano joined in 1977 as well and worked on odd hard to track projects like the balance board for Wii and the Nintendo 3DS Guide for Louvre.
After Miyamoto there are...
Masao Yamamoto joined in 1978 and may still be involved in support, though the last credit seems to be for Super Mario 3D Land.
Not at Nintendo anymore but still active is today's president of Creatures Hirokazu Tanaka who originally joined in 1980.
Toru Osawa joined in 1981 and is mainly involved with externally developed games.
Next active well known to the public veteran would be Yoshio Sakamoto who joined in 1982.