If you are using the default Ambience theme there are couple of config files you need to modify for changing the black tooltip color with the lightyellow one.
First lets identify file where background is defined:
$ grep -R "tooltip_bg_color" /usr/share/themes/Ambiance
you should be output with the following
/usr/share/themes/Ambiance/gtk-3.0/settings.ini:gtk-color-scheme = "base_color:#ffffff\nbg_color:#f2f1f0\ntooltip_bg_color:#000000\nselected_bg_color:#f07746\ntext_color:#3C3C3C\nfg_color:#4c4c4c\ntooltip_fg_color:#ffffff\nselected_fg_color:#ffffff\nlink_color:#DD4814\nbg_color_dark:#3c3b37\nfg_color_dark:#dfdbd2"
/usr/share/themes/Ambiance/gtk-3.0/gtk-main.css:@define-color tooltip_bg_color #f5f5b5;
/usr/share/themes/Ambiance/gtk-3.0/gtk-widgets.css: from (alpha (mix (@tooltip_bg_color, #ffffff, 0.2), 0.86)),
/usr/share/themes/Ambiance/gtk-3.0/gtk-widgets.css: to (alpha (@tooltip_bg_color, 0.86)));
/usr/share/themes/Ambiance/gtk-2.0/gtkrc:gtk-color-scheme = "base_color:#ffffff\nfg_color:#4c4c4c\ntooltip_fg_color:#000000\nselected_bg_color:#f07746\nselected_fg_color:#FFFFFF\ntext_color:#3C3C3C\nbg_color:#F2F1F0\ntooltip_bg_color:#f5f5b5\nlink_color:#DD4814"
/usr/share/themes/Ambiance/gtk-2.0/gtkrc: bg[NORMAL] = @tooltip_bg_color
/usr/share/themes/Ambiance/gtk-2.0/gtkrc: bg[SELECTED] = @tooltip_bg_color
We are interested with
/usr/share/themes/Ambiance/gtk-3.0/settings.ini/usr/share/themes/Ambiance/gtk-3.0/gtk-main.css
Now lets replace
tooltip_bg_color:#000000 with tooltip_bg_color:#f5f5b5, and
tooltip_fg_color:#ffffff with tooltip_fg_color:#000000
$ sudo sed -i 's/tooltip_bg_color:#000000/tooltip_bg_color:#f5f5bf/' /usr/share/themes/Ambiance/gtk-3.0/settings.ini
$ sudo sed -i 's/tooltip_fg_color:#ffffff/tooltip_fg_color:#000000/' /usr/share/themes/Ambiance/gtk-3.0/settings.ini
$ sudo sed -i 's/tooltip_bg_color #000000/tooltip_bg_color #f5f5b50/' /usr/share/themes/Ambiance/gtk-3.0/gtk-main.css
$ sudo sed -i 's/tooltip_bg_color #ffffff/tooltip_bg_color #000000/' /usr/share/themes/Ambiance/gtk-3.0/gtk-main.css
Finally you need to change theme to some other and back to Ambience and after that full restart of Eclipse is required (soft one (by File->Restart) may be not enough).